Annotations: 5IKK

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Arb2 domain-like	8045556	4004530	SCOP2 (2022-06-29)
A	SCOP2 Family	HDAC-like	8090954	4000427	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	alpha/beta-Hydrolases	8090953	3000102	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Arginase/deacetylase-like	8090955	3000260	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00850	e5ikkA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: PF00850	ECOD (1.6)
A	PF09757	e5ikkA2	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: PF09757	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00850	Histone deacetylase domain (Hist_deacetyl)	Histone deacetylase domain	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. ...	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1].	Domain
A	PF09757	Arb2-like domain (Arb2-like)	Arb2-like domain	This domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) (also known as histone deacetylase clr3) (EC:3.5.1.98) from S. pombe, its orthologue from S. cerevisiae HDA1, and similar sequences. This domain has been defined by sequence ho ...	This domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) (also known as histone deacetylase clr3) (EC:3.5.1.98) from S. pombe, its orthologue from S. cerevisiae HDA1, and similar sequences. This domain has been defined by sequence homology to the Arb2 protein from S. pombe (not included in this entry). Structure analysis reveals that the Arb2 domain has clear homology to alpha/beta-hydrolases but that it is lacking the catalytic triad of these enzymes. Functional studies show that the this domain is necessary for centromeric heterochromatin silencing suggesting a model where the Arb2-like domain, through residues N562 and Y563, acts as an anchor that connects the HDAC activity of Clr3 to the SHREC complex. SHREC (Snf2/Hdac Repressive) complex in fission yeast drives transcriptional gene silencing in heterochromatin [1]. Studies in HDA1 described that two Arb2-like domains form a compact homo-dimer via the arm elements, and assemble as an inverse 'V' shape and that the domain possesses histone binding ability [2,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Histone deacetylase clr3	deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity histone H3K14 deacetylase activity histone H3K deacetylase activity histone modifying activity catalytic activity	positive regulation of organelle organization regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process cellular component biogenesis chromatin organization organic substance biosynthetic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of chromosome organization positive regulation of organelle organization regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process cellular component biogenesis chromatin organization organic substance biosynthetic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of chromosome organization negative regulation of cellular biosynthetic process regulation of organelle organization positive regulation of chromosome organization regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of cellular component organization positive regulation of cellular component organization cellular biosynthetic process positive regulation of biological process protein-DNA complex organization cellular component organization positive regulation of heterochromatin formation organic substance metabolic process regulation of pericentric heterochromatin formation negative regulation of cellular process chromatin remodeling positive regulation of chromatin organization cellular component organization or biogenesis positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process positive regulation of pericentric heterochromatin formation heterochromatin formation protein-containing complex organization positive regulation of cellular component biogenesis epigenetic regulation of gene expression biological regulation chromosome organization regulation of macromolecule metabolic process gene expression regulation of cellular component biogenesis macromolecule biosynthetic process regulation of cellular biosynthetic process pericentric heterochromatin formation organelle organization negative regulation of biosynthetic process cellular process silent mating-type cassette heterochromatin formation regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II primary metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process nucleolar chromatin organization rDNA heterochromatin formation nucleus organization nucleolus organization facultative heterochromatin formation	protein-containing complex intracellular anatomical structure protein-DNA complex heterochromatin island chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus protein-containing complex intracellular anatomical structure protein-DNA complex heterochromatin island chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen chromosome, subtelomeric region chromosomal region chromosome, telomeric region subtelomeric heterochromatin mating-type region heterochromatin cytoplasm pericentric heterochromatin chromosome, centromeric region rDNA heterochromatin catalytic complex nuclear protein-containing complex histone deacetylase complex nucleoplasm ATPase complex transcription regulator complex SHREC complex NuRD complex SWI/SNF superfamily-type complex CHD-type complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR019154	Arb2-like domain	Domain
A	IPR000286	Histone deacetylase family	Family
A	IPR023801	Histone deacetylase domain	Domain
A	IPR017321	Histone deacetylase class II, yeast	Family
A	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.